GapMind for catabolism of small carbon sources

 

Aligments for a candidate for deoA in Shewanella loihica PV-4

Align uridine phosphorylase; EC 2.4.2.3 (characterized)
to candidate 5210964 Shew_3390 uridine phosphorylase (RefSeq)

Query= CharProtDB::CH_003939
         (253 letters)



>lcl|FitnessBrowser__PV4:5210964 Shew_3390 uridine phosphorylase
           (RefSeq)
          Length = 252

 Score =  385 bits (989), Expect = e-112
 Identities = 189/250 (75%), Positives = 218/250 (87%)

Query: 4   SDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTWRAELDGKPVI 63
           SDVFHLGLTK  L GATLAIVPGDP+RV++IA LMD P  LASHRE+T++ A +DGKP++
Sbjct: 2   SDVFHLGLTKEMLDGATLAIVPGDPERVKRIAELMDNPTFLASHREYTSYLAYIDGKPLV 61

Query: 64  VCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHINVGDVLVTTASVRLDGASLHF 123
           +CSTGIGGPSTSIAVEELAQLGI TFLR+GTTGAIQP +NVGDV+VT ASVRLDGASLHF
Sbjct: 62  ICSTGIGGPSTSIAVEELAQLGIDTFLRVGTTGAIQPQVNVGDVIVTQASVRLDGASLHF 121

Query: 124 APLEFPAVADFECTTALVEAAKSIGATTHVGVTASSDTFYPGQERYDTYSGRVVRHFKGS 183
           AP+EFPAVA+FECTTA+V A++  G   H+G+TASSDTFYPGQERYDT +GRV R F GS
Sbjct: 122 APMEFPAVANFECTTAMVAASREAGLEPHIGITASSDTFYPGQERYDTVTGRVTRRFAGS 181

Query: 184 MEEWQAMGVMNYEMESATLLTMCASQGLRAGMVAGVIVNRTQQEIPNAETMKQTESHAVK 243
           M+EWQ MGV+NYEMES+TL TMCA+QG RA  VAGVIVNRTQQEIP+  TMKQTE+ AV 
Sbjct: 182 MKEWQDMGVLNYEMESSTLFTMCATQGWRAACVAGVIVNRTQQEIPDEATMKQTETSAVS 241

Query: 244 IVVEAARRLL 253
           IVV AA++LL
Sbjct: 242 IVVAAAKKLL 251


Lambda     K      H
   0.318    0.131    0.375 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 259
Number of extensions: 5
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 253
Length of database: 252
Length adjustment: 24
Effective length of query: 229
Effective length of database: 228
Effective search space:    52212
Effective search space used:    52212
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory